Preferential interactions of the Escherichia coli LexA repressor with anions and protons are coupled to binding the recA operator.

The binding of Escherichia coli LexA repressor to the recA operator was examined as a function of the concentration of NaCl, KCl, NaF, and MgCl2 at pH 7.5, 21 degrees C. The effects of pH at 100 mM NaCl were also examined. Changes both in the qualitative appearance of the binding isotherms and in the magnitude of the apparent binding affinity with changes in solution conditions suggest that binding of anions and protons by LexA repressor is linked to oligomerization and/or operator binding. Binding of LexA repressor to the recA operator in the presence of NaCl ranging from 25 to 400 mM at picomolar DNA concentration showed a broad, apparently noncooperative, binding isotherm. Binding of LexA repressor in NaF at the same [DNA] yielded binding isotherms with a narrow transition, reflecting an apparently cooperative binding process. Also, the apparent binding affinity was weaker in NaF than in NaCl. Furthermore, the binding affinity and also the apparent binding mode, cooperative vs noncooperative, were pH dependent. The binding affinity of LexA repressor for operator was greatest near neutral pH. The apparent binding mode was noncooperative at pH 7-9 but was cooperative at pH 6 or 9.3. These observations suggest that the specific cation and anion composition and concentrations must be considered in understanding the details of regulation of the SOS system.

Equilibrium constants for nonspecific binding of proteins to DNA may be obtained by quantitative zonal DNA affinity chromatography.

Quantitative zonal DNA affinity chromatography may be used to determine accurate equilibrium constants for the binding of proteins nonspecifically to DNA. Zonal quantitative affinity chromatography has not previously been applied to the determination of binding constants of proteins to DNA, although its use is quite commonplace for determination of affinity constants for protein-protein or protein-small ligand interactions. Equilibrium constants were measured for the nonspecific binding of bovine pancreatic ribonuclease A and Escherichia coli lac repressor to double-stranded DNA immobilized on cellulose. The equilibrium constants determined agree with literature values evaluated using other techniques. The experimental advantages of the zonal technique, when it can be applied, are that collection of data is fast and data analysis is simple. Detection of the protein elution profile by absorbance at 220 nm with an in-line detector can provide adequate sensitivity when binding constants are in the range 10(2)-10(4) M-1.